Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Spi1

Cell type

Cell type Class
Neural
Cell type
Hippocampus
MeSH Description
A curved elevation of GRAY MATTER extending the entire length of the floor of the TEMPORAL HORN of the LATERAL VENTRICLE (see also TEMPORAL LOBE). The hippocampus proper, subiculum, and DENTATE GYRUS constitute the hippocampal formation. Sometimes authors include the ENTORHINAL CORTEX in the hippocampal formation.

Attributes by original data submitter

Sample

source_name
ChIP-Seq CKP25_PU.1
genotype/variation
CK-p25
age
4.5 months
tissue/cell type
hippocampus
chip antibody
PU.1 Santa Cruz Biotechnology sc-352x

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq: Hippocampi from 4.5 month old CK-p25 and age matched CK controls mice were isolated at 6 weeks after induction of p25 gene expression, and used for PU.1 ChIP-Seq. RNA-Seq: Hippocampi were isolated from the brains of mice at 3 and 4.5 months. Total RNA was extracted from FACS-purified CD11b+CD45 microglia using QIAGEN RNA Easy Mini Kit. ChIP-Seq: Libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Gjoneska et al., 2015) RNA-Seq: cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit and sequencing libraries were constructed using Nextera XT DNA library preparation kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
19393621
Reads aligned (%)
96.5
Duplicates removed (%)
14.8
Number of peaks
25008 (qval < 1E-05)

mm9

Number of total reads
19393621
Reads aligned (%)
96.2
Duplicates removed (%)
14.8
Number of peaks
25070 (qval < 1E-05)

Base call quality data from DBCLS SRA